Analyst loads blank (DAPI) channel


I am new to CellProfiler and CellProfiler Analyst, and I’ve been having problems figuring this out:

I have a DAPI and RFP channel for each image. The Classifier fetches images without displaying an error. However, while it displays the RFP image fine, the DAPI channel is blank (even when I assign the RFP colour as “none”). Same problem when using the ImageViewer.

I have checked that the path and file columns are correct, and the database was exported as a single object table.
I have also checked that each channels have colours assigned to them.

The DAPI channel seems to be displayed fine on the CellProfiler image viewer, just not on the Analyst image viewer.

I will copy the properties file at the end, since I can’t upload .properties.

Thank you for your help.


CellProfiler Analyst 2.0 properties file


==== Database Info ====

db_type = sqlite
db_sqlite_file = D:\Nanopattern images\n=6,7\CK Nanopattern\Nanopattern Test Run.db

==== Database Tables ====

image_table = Per_Image
object_table = Per_Object

==== Database Columns ====

image_id = ImageNumber
object_id = ObjectNumber
plate_id = Image_Metadata_Plate
well_id = Image_Metadata_Well

cell_x_loc = Nuclei_Location_Center_X
cell_y_loc = Nuclei_Location_Center_Y

==== Image Path and File Name Columns ====

image_path_cols = Image_PathName_DAPI,Image_PathName_RFP
image_file_cols = Image_FileName_DAPI,Image_FileName_RFP
image_thumbnail_cols =
image_names = DAPI,RFP
image_channel_colors = blue,red

==== Image Accesss Info ====

image_url_prepend =

==== Dynamic Groups ====

==== Image Filters ====

==== Meta data ====

object_name = cell, cells,

plate_shape = 8,12
well_format = A01

==== Excluded Columns ====

classifier_ignore_columns = table_number_key_column, image_number_key_column, object_number_key_column

==== Other ====

image_tile_size = 100

======== Auto Load Training Set ========

training_set =

======== Area Based Scoring ========

area_scoring_column =

======== Output Per-Object Classes ========

class_table =

======== Check Tables ========

check_tables = yes

I’ve figured it out.

The images I was trying to load had colour applied to it, so it was detecting 3 channels, and only loading the first channel (the black red channel). I had to convert the images to grayscale and it loaded fine.

Great, though sorry for our lack of reply. In any case, thanks for writing back.